Chronic fatigue syndrome (CFS) is a debilitating illness characterized by long-term fatigue and by other symptoms such as impaired memory or concentration, sore throat, tender lymph nodes, muscle pain, multi-joint pain, new headaches, unrefreshing sleep, and exercise intolerance. Individuals with CFS often exhibit gastrointestinal symptoms. While the cause(s) of chronic fatigue syndrome has not been established, a number of outbreaks implicate an infectious etiology. CFS patients exhibit both chronic activation and dysfunction of their immune systems. Increased levels of inflammatory cytokines could engender many of the symptoms of the illness. Cross-talk is known to occur between the intestinal immune cells and the microbes that reside in the gut. An altered community of gut microbes due to a dysfunctional immune system could be responsible for some CFS symptoms and contribute to chronic immune activation by affecting mucosal immunity and by disrupting intestinal integrity, thus allowing translocation of bacteria into blood from the gut. We will determine whether the types of bacteria found in the blood and gut differ between CFS patients and healthy individuals. The bacterial composition of the blood and gut microbiomes will be determined in 48 chronically ill individuals and compared to 24 healthy controls by pyrosequencing and analysis of 16S rDNA sequences. Assays will be performed to assess the expression levels of genes relevant to the immune system in human cells shed from the intestine. The amount of lactoferrin in stool samples will be determined as a measure of inflammation and bacterial endotoxin as an indication of intestinal dysfunction. Canonical correlation analysis will be used to identify correlated bacterial taxa and patterns of gene expression within patient subsets vs. healthy individuals. Such exploratory studies might suggest therapies to shift the gut microbiome toward that of healthier individuals in the hopes of ameliorating symptoms and could reveal whether trials of probiotics and antimicrobial or particular inflammation-modulating drugs may be warranted. Because characterization of the human microbiota is just beginning, our analyses will also make a valuable contribution to knowledge about the diversity of microbes associated with CFS.